Re: [ccp4bb] 8/ 2263 spots indexed XDS

Hi Almu, I have yet to see a data set with clear reflections that cannot be indexed with XDS. The most often reason for failure is some wrong input, most often ORGX/ORGY and ROTATION_AXIS, but of course OSCILLATION_RANGE, X-RAY_WAVELENGTH, DETECTOR_DISTANCE must also be correct. If you cannot

Re: [ccp4bb] microscope camera

There are CCD modules (often come with lenses, which can be taken off) sold on Amazon, eBay or aliexpress (or even better, Taobao) costing USD 20-40. These modules should be capable of taking full HD movies (MPEG or YUV2 compressed) at 30fps these days. Some may allow 120fps@640x480 or promise

Re: [ccp4bb] microscope camera

There are fairly cheap adapter eye-pieces that can be purchased that will hold most of the standard phones (iPhones 5, 6, 7, etc). They work very well and we have replaced our old microscope camera with these and the pictures are great (for one offs, not for taking time courses over many

Re: [ccp4bb] microscope camera

With a little fiddling and patience, one can just point a cell phone camera down the eyepiece. It doesn’t produce the best pics, but works fine if you just want to stick a few in a notebook (or a grant …). From: CCP4 bulletin board on behalf of Sergei Strelkov Reply-To: Sergei Strelkov

Re: [ccp4bb] technical question

Or use the residue name MHO if SME has the wrong hand around the sulfur. Cheers, Robbie On 29 Nov 2019 21:47, Paul Emsley wrote: On 29/11/2019 18:06, amit gaur wrote: > I want to replace a particular methionine in a pdbwith methionine sulfoxide( > an oxidized form of > methionine). Can body

Re: [ccp4bb] technical question

On 29/11/2019 18:06, amit gaur wrote: I want to replace a particular methionine in a pdbwith methionine sulfoxide( an oxidized form of methionine). Can body please tell me how to do this? I am familiar with pymol, chimera and coot software. In Coot: Extensions -> Modelling -> Replace Residue

Re: [ccp4bb] space group "P 21 21 2 A"?

Thank you very much El vie., 29 de nov. de 2019 a la(s) 12:40, Eleanor Dodson ( eleanor.dod...@york.ac.uk) escribió: > That is a code for P21 21 2 symmetry where the origin is positioned at > 1/4,0,0 > The sym ops in the PDB header presumably reflect that.. > > > On Fri, 29 Nov 2019 at 18:16,

Re: [ccp4bb] space group "P 21 21 2 A"?

That is a code for P21 21 2 symmetry where the origin is positioned at 1/4,0,0 The sym ops in the PDB header presumably reflect that.. On Fri, 29 Nov 2019 at 18:16, Murpholino Peligro wrote: > Entry 1gzx has space group P 21 21 2 A ( > https://www.rcsb.org/structure/1gzx) > I am lost! > This

[ccp4bb] technical question

Hi everbody, I want to replace a particular methionine in a pdb with methionine sulfoxide( an oxidized form of methionine). Can body please tell me how to do this? I am familiar with pymol, chimera and coot software. -- *Amit Gaur* *Post Doctoral ResearcherThomas Jefferson University* *1020,

[ccp4bb] space group "P 21 21 2 A"?

Entry 1gzx has space group P 21 21 2 A (https://www.rcsb.org/structure/1gzx) I am lost! This is the first time that I see a letter at the end of a (protein) space group. Can somebody explain this? Please. Thanks To

Re: [ccp4bb] 8/ 2263 spots indexed XDS

Thank you Tim, I will try and let you know how it goes. All the best, Almudena El vie., 29 nov. 2019 a las 14:43, Tim Gruene () escribió: > Dear Almudena, > > SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to > increase in your situation. The default is 3. Try e.g. 5,

[ccp4bb] RES: [ccp4bb] Xray-dataset usable despite low completeness ?

Lol __ Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A sorte acompanha uma mente bem treinada"

Re: [ccp4bb] 8/ 2263 spots indexed XDS

Dear Almudena, SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to increase in your situation. The default is 3. Try e.g. 5, and increase slowly to make sure that the suggested solution makes sense Best regards, Tim On Friday, November 29, 2019 12:48:11 PM CET Almudena

[ccp4bb] AW: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS

Dear Almu, were your data collected at a synchrotron? Many synchrotrons run automatic processing of the data being collected and it is worth looking if there is some processing directory between the frames you collected. If so, these data may already be quite decent, and in any case, the

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Re: [ccp4bb] 8/ 2263 spots indexed XDS

Hi Almudena I wouldn't claim to be a great expert on XDS, but, based on the experience of analyzing a load of data on the beamline, there are many things you can try - The most important ones are to use lots (all?) your images for the spot search (SPOT_RANGE) , and not to hesitate cutting the

[ccp4bb] 8/ 2263 spots indexed XDS

Dear all, I have some data sets that don't want to be processed :p In one of them, when I look at IDXREF.LP I see virtually none of the found spots were indexed and the reason is that they are "too far from the expected position". The spots are smeary and elongated, so not the prettiest. I have

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